package edu.protbioinfo;

import java.io.IOException;
import java.io.PrintStream;
import java.text.NumberFormat;

import edu.protbioinfo.Utils.Pair;

public class SequenceAlignment {
	public static final char BLANK = '-';
	private Pair<String, String> alignment = new Pair<String, String>("", "");
	private double score;
	
	public Pair<String, String> getAlignment() {
		return alignment;
	}
	
	public void setAlignment(Pair<String, String> alignment) {
		this.alignment = alignment;
	}
	
	public double getScore() {
		return score;
	}
	
	public void setScore(double score) {
		this.score = score;
	}
	
	public String toPrettyString(){
		StringBuffer sb = new StringBuffer();
		String newLine = System.getProperty("line.separator");
		
		sb.append("Score:" + score + newLine);
		sb.append("Alignment:" + newLine);
		sb.append(alignment.first() + newLine);
		sb.append(alignment.second() + newLine);
		
		return sb.toString();
	}
	
}
